X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=cb78b042090fcf44b3a2cb1ff06b4d4f1db55320;hb=bfb4b56a77352694f4bc445ec31851bbdcdce140;hp=cae5da29d277c6be93ea1c3cc806ed3baaed32a8;hpb=60f7107d9fc77f34e96ae4b9780e2d11195aed3b;p=jalview.git
diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index cae5da2..cb78b04 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -1,28 +1,33 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
-
package jalview.analysis;
-import java.util.*;
-
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
import jalview.util.Format;
-import jalview.datamodel.*;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
/**
* Takes in a vector or array of sequences and column start and column end and
@@ -35,6 +40,8 @@ import jalview.datamodel.*;
*/
public class StructureFrequency
{
+ public static final int STRUCTURE_PROFILE_LENGTH = 74;
+
// No need to store 1000s of strings which are not
// visible to the user.
public static final String MAXCOUNT = "C";
@@ -60,15 +67,15 @@ public class StructureFrequency
*/
public static int findPair(SequenceFeature[] pairs, int indice)
{
- System.out.print("indice"+indice+" ");
+
for (int i = 0; i < pairs.length; i++)
{
if (pairs[i].getBegin() == indice)
-
+
{
- System.out.println(pairs[i].getEnd());
+
return pairs[i].getEnd();
-
+
}
}
return -1;
@@ -89,19 +96,11 @@ public class StructureFrequency
int end, Hashtable[] result, boolean profile,
AlignmentAnnotation rnaStruc)
{
-// System.out.println("longueur="+sequences.length);
-// for(int l=0;l<=(sequences.length-1);l++){
-// System.out.println("sequences "+l+":"+sequences[l].getSequenceAsString());
-// }
-// System.out.println("start="+start);
- System.out.println("end="+end);
-// System.out.println("result="+result.length);
-//
-// System.out.println("profile="+profile);
-// System.out.println("rnaStruc="+rnaStruc);
+
Hashtable residueHash;
String maxResidue;
char[] struc = rnaStruc.getRNAStruc().toCharArray();
+
SequenceFeature[] rna = rnaStruc._rnasecstr;
char c, s, cEnd;
int count = 0, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
@@ -109,7 +108,6 @@ public class StructureFrequency
int[][] pairs;
float percentage;
boolean wooble = true;
-
for (i = start; i < end; i++) // foreach column
{
residueHash = new Hashtable();
@@ -117,11 +115,11 @@ public class StructureFrequency
values = new int[255];
pairs = new int[255][255];
bpEnd = -1;
- //System.out.println("s="+struc[i]);
+ // System.out.println("s="+struc[i]);
if (i < struc.length)
{
s = struc[i];
-
+
}
else
{
@@ -141,76 +139,74 @@ public class StructureFrequency
}
else
{
-
-
+
bpEnd = findPair(rna, i);
-
- if (bpEnd>-1)
- {
- for (j = 0; j < jSize; j++) // foreach row
+
+ if (bpEnd > -1)
{
- if (sequences[j] == null)
+ for (j = 0; j < jSize; j++) // foreach row
{
- System.err
- .println("WARNING: Consensus skipping null sequence - possible race condition.");
- continue;
- }
- c = sequences[j].getCharAt(i);
- //System.out.println("c="+c);
-
+ if (sequences[j] == null)
+ {
+ System.err
+ .println("WARNING: Consensus skipping null sequence - possible race condition.");
+ continue;
+ }
+ c = sequences[j].getCharAt(i);
+ // System.out.println("c="+c);
// standard representation for gaps in sequence and structure
if (c == '.' || c == ' ')
{
- System.err
- .println("WARNING: Consensus skipping null sequence - possible race condition.");
+ c = '-';
+ }
+
+ if (c == '-')
+ {
+ values['-']++;
continue;
}
cEnd = sequences[j].getCharAt(bpEnd);
-
-
- System.out.println("pairs ="+c+","+cEnd);
- if (checkBpType(c, cEnd)==true)
+
+ // System.out.println("pairs ="+c+","+cEnd);
+ if (checkBpType(c, cEnd) == true)
{
values['(']++; // H means it's a helix (structured)
maxResidue = "(";
- wooble=true;
- System.out.println("It's a pair wc");
-
+ wooble = true;
+ // System.out.println("It's a pair wc");
+
}
- if (checkBpType(c, cEnd)==false)
+ if (checkBpType(c, cEnd) == false)
{
- wooble =false;
+ wooble = false;
values['[']++; // H means it's a helix (structured)
maxResidue = "[";
- System.out.println("It's an pair non canonic");
- System.out.println(sequences[j].getRNA());
- System.out.println(rnaStruc.getRNAStruc().charAt(i));
+
}
- pairs[c][cEnd]++;
-
-
- }
+ pairs[c][cEnd]++;
+ }
}
// nonGap++;
}
// UPDATE this for new values
if (profile)
{
+ // TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
residueHash.put(PROFILE, new int[][]
{ values, new int[]
{ jSize, (jSize - values['-']) } });
residueHash.put(PAIRPROFILE, pairs);
}
- if (wooble==true)
+ if (wooble == true)
{
- count = values['('];
+ count = values['('];
}
- if (wooble==false)
+ if (wooble == false)
{
- count = values['['];
+ count = values['['];
}
residueHash.put(MAXCOUNT, new Integer(count));
residueHash.put(MAXRESIDUE, maxResidue);
@@ -226,18 +222,20 @@ public class StructureFrequency
}
if (bpEnd > 0)
{
- values[')'] = values['('];
+ values[')'] = values['('];
values[']'] = values['['];
values['('] = 0;
values['['] = 0;
residueHash = new Hashtable();
- if (wooble==true){
- System.out.println(maxResidue+","+wooble);
- maxResidue = ")";
+ if (wooble == true)
+ {
+ // System.out.println(maxResidue+","+wooble);
+ maxResidue = ")";
}
- if(wooble==false){
- System.out.println(maxResidue+","+wooble);
- maxResidue = "]";
+ if (wooble == false)
+ {
+ // System.out.println(maxResidue+","+wooble);
+ maxResidue = "]";
}
if (profile)
{
@@ -255,6 +253,7 @@ public class StructureFrequency
residueHash.put(PID_GAPS, new Float(percentage));
result[bpEnd] = residueHash;
+
}
}
}
@@ -355,18 +354,19 @@ public class StructureFrequency
// initialised properly
return;
}
- String fmtstr="%3.1f";
- int precision=2;
- while (nseq>100) {
+ String fmtstr = "%3.1f";
+ int precision = 2;
+ while (nseq > 100)
+ {
precision++;
- nseq/=10;
+ nseq /= 10;
}
- if (precision>2)
+ if (precision > 2)
{
- fmtstr = "%"+(2+precision)+"."+precision+"f";
+ fmtstr = "%" + (2 + precision) + "." + precision + "f";
}
Format fmt = new Format(fmtstr);
-
+
for (int i = iStart; i < width; i++)
{
Hashtable hci;
@@ -443,7 +443,8 @@ public class StructureFrequency
tval = (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0]
- + (char) ((int[]) ca[c])[1] + " " + fmt.form(tval) + "%";
+ + (char) ((int[]) ca[c])[1] + " " + fmt.form(tval)
+ + "%";
p++;
}
@@ -469,16 +470,19 @@ public class StructureFrequency
public static int[] extractProfile(Hashtable hconsensus,
boolean ignoreGapsInConsensusCalculation)
{
- int[] rtnval = new int[74]; // 2*(5*5)+2
+ int[] rtnval = new int[STRUCTURE_PROFILE_LENGTH]; // 2*(5*5)+2
int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
int[][] pairs = (int[][]) hconsensus
.get(StructureFrequency.PAIRPROFILE);
if (profile == null)
+ {
return null;
+ }
// TODO fix the object length, also do it in completeConsensus
- Object[] ca = new Object[625];
+ // Object[] ca = new Object[625];
+ int[][] ca = new int[625][];
float[] vl = new float[625];
int x = 0;
for (int c = 65; c < 90; c++)
@@ -493,21 +497,28 @@ public class StructureFrequency
}
jalview.util.QuickSort.sort(vl, ca);
- rtnval[0] = 2;
+ int valuesCount = 0;
rtnval[1] = 0;
+ int offset = 2;
for (int c = 624; c > 0; c--)
{
if (vl[c] > 0)
{
- rtnval[rtnval[0]++] = ((int[]) ca[c])[0];
- rtnval[rtnval[0]++] = ((int[]) ca[c])[1];
- rtnval[rtnval[0]] = (int) (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
+ rtnval[offset++] = ca[c][0];
+ rtnval[offset++] = ca[c][1];
+ rtnval[offset] = (int) (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
- rtnval[1] += rtnval[rtnval[0]++];
+ rtnval[1] += rtnval[offset++];
+ valuesCount++;
}
}
+ rtnval[0] = valuesCount;
- return rtnval;
+ // insert profile type code in position 0
+ int[] result = new int[rtnval.length + 1];
+ result[0] = AlignmentAnnotation.STRUCTURE_PROFILE;
+ System.arraycopy(rtnval, 0, result, 1, rtnval.length);
+ return result;
}
public static void main(String args[])